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@kortschak
kortschak committed Mar 29, 2012
1 parent e134608 commit a4d7bff
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Showing 113 changed files with 351 additions and 351 deletions.
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -2,7 +2,7 @@

##Installation

$ go get github.com/kortschak/BioGo/...
$ go get github.com/kortschak/biogo/...

##Overview

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2 changes: 1 addition & 1 deletion align/align.go
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Expand Up @@ -17,7 +17,7 @@ package align
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/seq"
"github.com/kortschak/biogo/seq"
)

type Aligner interface {
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2 changes: 1 addition & 1 deletion align/nw/example_test.go
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Expand Up @@ -17,7 +17,7 @@ package nw

import (
"fmt"
"github.com/kortschak/BioGo/seq"
"github.com/kortschak/biogo/seq"
)

func ExampleAligner_Align() {
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6 changes: 3 additions & 3 deletions align/nw/nw.go
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Expand Up @@ -17,9 +17,9 @@ package nw
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/bio"
"github.com/kortschak/BioGo/seq"
"github.com/kortschak/BioGo/util"
"github.com/kortschak/biogo/bio"
"github.com/kortschak/biogo/seq"
"github.com/kortschak/biogo/util"
)

// Default character table lookups.
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2 changes: 1 addition & 1 deletion align/nw/nw_test.go
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Expand Up @@ -16,7 +16,7 @@ package nw
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/io/seqio/fasta"
"github.com/kortschak/biogo/io/seqio/fasta"
check "launchpad.net/gocheck"
"testing"
)
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6 changes: 3 additions & 3 deletions align/pals/dp/align.go
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Expand Up @@ -17,9 +17,9 @@ package dp
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/align/pals/filter"
"github.com/kortschak/BioGo/bio"
"github.com/kortschak/BioGo/seq"
"github.com/kortschak/biogo/align/pals/filter"
"github.com/kortschak/biogo/bio"
"github.com/kortschak/biogo/seq"
"sort"
)

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8 changes: 4 additions & 4 deletions align/pals/dp/dp_test.go
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Expand Up @@ -16,10 +16,10 @@ package dp
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/align/pals/filter"
"github.com/kortschak/BioGo/align/sw"
"github.com/kortschak/BioGo/seq"
"github.com/kortschak/BioGo/util"
"github.com/kortschak/biogo/align/pals/filter"
"github.com/kortschak/biogo/align/sw"
"github.com/kortschak/biogo/seq"
"github.com/kortschak/biogo/util"
check "launchpad.net/gocheck"
"testing"
)
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4 changes: 2 additions & 2 deletions align/pals/dp/kernel.go
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Expand Up @@ -16,8 +16,8 @@ package dp
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/align/pals/filter"
"github.com/kortschak/BioGo/seq"
"github.com/kortschak/biogo/align/pals/filter"
"github.com/kortschak/biogo/seq"
)

const (
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4 changes: 2 additions & 2 deletions align/pals/dp/lookup.go
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Expand Up @@ -16,8 +16,8 @@ package dp
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/bio"
"github.com/kortschak/BioGo/util"
"github.com/kortschak/biogo/bio"
"github.com/kortschak/biogo/util"
)

var lookUp util.CTL
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8 changes: 4 additions & 4 deletions align/pals/filter/filter.go
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Expand Up @@ -19,10 +19,10 @@ package filter
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/bio"
"github.com/kortschak/BioGo/index/kmerindex"
"github.com/kortschak/BioGo/morass"
"github.com/kortschak/BioGo/seq"
"github.com/kortschak/biogo/bio"
"github.com/kortschak/biogo/index/kmerindex"
"github.com/kortschak/biogo/morass"
"github.com/kortschak/biogo/seq"
)

// Ukonnen's Lemma: U(n, q, 𝛜) := (n + 1) - q(⌊𝛜n⌋ + 1)
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8 changes: 4 additions & 4 deletions align/pals/filter/filter_test.go
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Expand Up @@ -16,10 +16,10 @@ package filter
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/index/kmerindex"
"github.com/kortschak/BioGo/morass"
"github.com/kortschak/BioGo/seq"
"github.com/kortschak/BioGo/util"
"github.com/kortschak/biogo/index/kmerindex"
"github.com/kortschak/biogo/morass"
"github.com/kortschak/biogo/seq"
"github.com/kortschak/biogo/util"
check "launchpad.net/gocheck"
"testing"
)
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4 changes: 2 additions & 2 deletions align/pals/filter/lookup.go
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Expand Up @@ -16,8 +16,8 @@ package filter
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/bio"
"github.com/kortschak/BioGo/util"
"github.com/kortschak/biogo/bio"
"github.com/kortschak/biogo/util"
)

var lookUp util.CTL
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4 changes: 2 additions & 2 deletions align/pals/filter/merge.go
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Expand Up @@ -16,8 +16,8 @@ package filter
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/index/kmerindex"
"github.com/kortschak/BioGo/seq"
"github.com/kortschak/biogo/index/kmerindex"
"github.com/kortschak/biogo/seq"
"sort"
)

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4 changes: 2 additions & 2 deletions align/pals/packseqs.go
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Expand Up @@ -18,8 +18,8 @@ package pals
import (
"bytes"
"fmt"
"github.com/kortschak/BioGo/seq"
"github.com/kortschak/BioGo/util"
"github.com/kortschak/biogo/seq"
"github.com/kortschak/biogo/util"
)

var (
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8 changes: 4 additions & 4 deletions align/pals/pair.go
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Expand Up @@ -17,10 +17,10 @@ package pals

import (
"fmt"
"github.com/kortschak/BioGo/align/pals/dp"
"github.com/kortschak/BioGo/bio"
"github.com/kortschak/BioGo/feat"
"github.com/kortschak/BioGo/seq"
"github.com/kortschak/biogo/align/pals/dp"
"github.com/kortschak/biogo/bio"
"github.com/kortschak/biogo/feat"
"github.com/kortschak/biogo/seq"
)

// A FeaturePair holds a pair of features with additional information relating the two.
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14 changes: 7 additions & 7 deletions align/pals/pals.go
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Expand Up @@ -17,13 +17,13 @@ package pals
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/align/pals/dp"
"github.com/kortschak/BioGo/align/pals/filter"
"github.com/kortschak/BioGo/bio"
"github.com/kortschak/BioGo/index/kmerindex"
"github.com/kortschak/BioGo/morass"
"github.com/kortschak/BioGo/seq"
"github.com/kortschak/BioGo/util"
"github.com/kortschak/biogo/align/pals/dp"
"github.com/kortschak/biogo/align/pals/filter"
"github.com/kortschak/biogo/bio"
"github.com/kortschak/biogo/index/kmerindex"
"github.com/kortschak/biogo/morass"
"github.com/kortschak/biogo/seq"
"github.com/kortschak/biogo/util"
"io"
"os"
"unsafe"
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8 changes: 4 additions & 4 deletions align/pals/pals_test.go
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Expand Up @@ -18,10 +18,10 @@ package pals
import (
"bytes"
"fmt"
"github.com/kortschak/BioGo/align/pals/dp"
"github.com/kortschak/BioGo/align/pals/filter"
"github.com/kortschak/BioGo/seq"
"github.com/kortschak/BioGo/util"
"github.com/kortschak/biogo/align/pals/dp"
"github.com/kortschak/biogo/align/pals/filter"
"github.com/kortschak/biogo/seq"
"github.com/kortschak/biogo/util"
check "launchpad.net/gocheck"
"math"
"testing"
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4 changes: 2 additions & 2 deletions align/pals/write.go
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Expand Up @@ -17,8 +17,8 @@ package pals

import (
"fmt"
"github.com/kortschak/BioGo/feat"
"github.com/kortschak/BioGo/io/featio/gff"
"github.com/kortschak/biogo/feat"
"github.com/kortschak/biogo/io/featio/gff"
"io"
"os"
)
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2 changes: 1 addition & 1 deletion align/sw/example_test.go
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Expand Up @@ -17,7 +17,7 @@ package sw

import (
"fmt"
"github.com/kortschak/BioGo/seq"
"github.com/kortschak/biogo/seq"
)

func ExampleAligner_Align() {
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6 changes: 3 additions & 3 deletions align/sw/sw.go
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Expand Up @@ -17,9 +17,9 @@ package sw
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/bio"
"github.com/kortschak/BioGo/seq"
"github.com/kortschak/BioGo/util"
"github.com/kortschak/biogo/bio"
"github.com/kortschak/biogo/seq"
"github.com/kortschak/biogo/util"
)

// Default character table lookups.
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2 changes: 1 addition & 1 deletion align/sw/sw_test.go
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Expand Up @@ -16,7 +16,7 @@ package sw
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/io/seqio/fasta"
"github.com/kortschak/biogo/io/seqio/fasta"
check "launchpad.net/gocheck"
"testing"
)
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2 changes: 1 addition & 1 deletion alphabet/alphabet.go
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Expand Up @@ -18,7 +18,7 @@ package alphabet
import (
"errors"
"fmt"
"github.com/kortschak/BioGo/bio"
"github.com/kortschak/biogo/bio"
"sort"
"strings"
"unicode"
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4 changes: 2 additions & 2 deletions bio/defs.go
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Expand Up @@ -17,6 +17,6 @@ package bio

// Output defaults.
var (
Precision = 4 // BioGo global precision value.
FloatFormat byte = 'f' // BioGo global float format.
Precision = 4 // biogo global precision value.
FloatFormat byte = 'f' // biogo global float format.
)
4 changes: 2 additions & 2 deletions bio/errors_test.go
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Expand Up @@ -35,9 +35,9 @@ func (s *S) TestCaller(c *check.C) {
err := NewError("message", 0, "item")
c.Check(err.Error(), check.Equals, "message")
fn, ln := err.FileLine()
c.Check(fn, check.Matches, "/.*/BioGo/bio/errors_test.go")
c.Check(fn, check.Matches, "/.*/biogo/bio/errors_test.go")
c.Check(ln, check.Equals, 35)
c.Check(err.Package(), check.Equals, "github.com/kortschak/BioGo/bio.(*S)")
c.Check(err.Package(), check.Equals, "github.com/kortschak/biogo/bio.(*S)")
c.Check(err.Function(), check.Equals, "TestCaller")
err = f(5).(Error)
fmt.Println(err.Tracef(10))
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4 changes: 2 additions & 2 deletions concurrent/map.go
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Expand Up @@ -16,8 +16,8 @@ package concurrent
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/bio"
"github.com/kortschak/BioGo/util"
"github.com/kortschak/biogo/bio"
"github.com/kortschak/biogo/util"
"math"
)

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2 changes: 1 addition & 1 deletion concurrent/processor.go
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Expand Up @@ -16,7 +16,7 @@ package concurrent
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/bio"
"github.com/kortschak/biogo/bio"
"runtime"
"sync"
)
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2 changes: 1 addition & 1 deletion concurrent/promise.go
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Expand Up @@ -16,7 +16,7 @@ package concurrent
// along with this program. If not, see <http://www.gnu.org/licenses/>.

import (
"github.com/kortschak/BioGo/bio"
"github.com/kortschak/biogo/bio"
"sync"
)

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2 changes: 1 addition & 1 deletion doc.go
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Expand Up @@ -201,4 +201,4 @@ PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program. If not, see <http:www.gnu.org/licenses/>.
*/
package BioGo
package biogo
8 changes: 4 additions & 4 deletions examples/brahma/main.go
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Expand Up @@ -5,10 +5,10 @@ import (
"encoding/gob"
"flag"
"fmt"
"github.com/kortschak/BioGo/feat"
"github.com/kortschak/BioGo/interval"
"github.com/kortschak/BioGo/io/featio/gff"
"github.com/kortschak/BioGo/util"
"github.com/kortschak/biogo/feat"
"github.com/kortschak/biogo/interval"
"github.com/kortschak/biogo/io/featio/gff"
"github.com/kortschak/biogo/util"
"os"
"runtime"
"sort"
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8 changes: 4 additions & 4 deletions examples/cgr/main.go
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Expand Up @@ -3,10 +3,10 @@ package main
import (
"flag"
"fmt"
"github.com/kortschak/BioGo/graphics/color"
"github.com/kortschak/BioGo/graphics/kmercolor"
"github.com/kortschak/BioGo/index/kmerindex"
"github.com/kortschak/BioGo/io/seqio/fasta"
"github.com/kortschak/biogo/graphics/color"
"github.com/kortschak/biogo/graphics/kmercolor"
"github.com/kortschak/biogo/index/kmerindex"
"github.com/kortschak/biogo/io/seqio/fasta"
"image/png"
"os"
)
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4 changes: 2 additions & 2 deletions examples/distance/main.go
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Expand Up @@ -3,8 +3,8 @@ package main
import (
"flag"
"fmt"
"github.com/kortschak/BioGo/index/kmerindex"
"github.com/kortschak/BioGo/io/seqio/fasta"
"github.com/kortschak/biogo/index/kmerindex"
"github.com/kortschak/biogo/io/seqio/fasta"
"os"
)

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6 changes: 3 additions & 3 deletions examples/ganesh/main.go
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Expand Up @@ -4,9 +4,9 @@ import (
"bufio"
"flag"
"fmt"
"github.com/kortschak/BioGo/matrix"
"github.com/kortschak/BioGo/matrix/sparse"
"github.com/kortschak/BioGo/nmf"
"github.com/kortschak/biogo/matrix"
"github.com/kortschak/biogo/matrix/sparse"
"github.com/kortschak/biogo/nmf"
"io"
"math/rand"
"os"
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10 changes: 5 additions & 5 deletions examples/gayatri/main.go
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Expand Up @@ -3,11 +3,11 @@ package main
import (
"flag"
"fmt"
"github.com/kortschak/BioGo/index/kmerindex"
"github.com/kortschak/BioGo/io/seqio/fasta"
"github.com/kortschak/BioGo/matrix"
"github.com/kortschak/BioGo/matrix/sparse"
"github.com/kortschak/BioGo/nmf"
"github.com/kortschak/biogo/index/kmerindex"
"github.com/kortschak/biogo/io/seqio/fasta"
"github.com/kortschak/biogo/matrix"
"github.com/kortschak/biogo/matrix/sparse"
"github.com/kortschak/biogo/nmf"
"math/rand"
"os"
"runtime"
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